SMTL ID : 4m09.1

Crystal Structure of Mutant Chlorite Dismutase from Candidatus Nitrospira defluvii W146Y R173Q

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-pentamer

Ligands

5 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 24 residues within 4Å: Chain A: P.111, T.112, Y.113, V.114, F.117, L.125, I.142, K.144, W.148, M.160, H.163, T.164, A.167, L.171, Q.176, L.178, F.189, T.191, F.193, L.204, L.208, F.220 Chain B: R.206 Ligands: IMD.4 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:V.114, A:F.117, A:L.125, A:L.125, A:A.167, A:L.171, A:Q.176, A:L.178, A:F.189, A:T.191, A:F.193, A:F.193, A:L.208, A:F.220 Hydrogen bonds: A:T.112, A:Y.113, A:V.114 Salt bridges: A:K.144, B:R.206 Metal complexes: A:H.163 HEM.6: 21 residues within 4Å: Chain B: P.111, T.112, Y.113, V.114, F.117, I.140, I.142, K.144, W.148, M.160, H.163, T.164, A.167, Q.176, L.178, F.189, T.191, F.193, L.204, L.208, F.220 22 PLIP interactions: 20 interactions with chain B, 2 interactions with chain D, Hydrophobic interactions: B:V.114, B:F.117, B:I.140, B:A.167, B:Q.176, B:L.178, B:F.189, B:F.189, B:T.191, B:F.193, B:L.204, B:L.208, B:F.220 Hydrogen bonds: B:T.112, B:Y.113, B:V.114 Water bridges: B:T.112, D:R.206 Salt bridges: B:K.144, D:R.206 pi-Stacking: B:H.163 Metal complexes: B:H.163 HEM.10: 24 residues within 4Å: Chain A: R.206 Chain C: P.111, T.112, Y.113, V.114, F.117, L.125, I.140, I.142, K.144, W.148, M.160, H.163, T.164, A.167, L.171, Q.176, L.178, F.189, T.191, F.193, L.208, F.220 Ligands: EDO.15 19 PLIP interactions: 18 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:F.117, C:L.125, C:I.140, C:A.167, C:L.171, C:Q.176, C:L.178, C:F.189, C:F.189, C:F.189, C:T.191, C:F.193, C:L.208, C:F.220 Hydrogen bonds: C:T.112, C:Y.113, C:V.114 Metal complexes: C:H.163 Salt bridges: A:R.206 HEM.16: 23 residues within 4Å: Chain D: P.111, T.112, Y.113, V.114, L.125, I.140, I.142, K.144, W.148, M.160, H.163, T.164, A.167, L.171, L.178, F.189, T.191, F.193, L.204, L.208, F.220 Chain E: R.206 Ligands: IMD.17 22 PLIP interactions: 21 interactions with chain D, 1 interactions with chain E, Hydrophobic interactions: D:L.125, D:I.140, D:T.164, D:A.167, D:L.171, D:L.178, D:F.189, D:F.189, D:F.189, D:T.191, D:F.193, D:F.193, D:L.204, D:L.208, D:F.220 Hydrogen bonds: D:T.112, D:Y.113, D:V.114 Salt bridges: D:K.144, E:R.206 pi-Stacking: D:H.163 Metal complexes: D:H.163 HEM.21: 23 residues within 4Å: Chain C: R.206 Chain E: P.111, T.112, Y.113, V.114, I.142, K.144, W.148, M.160, H.163, T.164, A.167, L.171, V.174, Q.176, L.178, F.189, T.191, F.193, L.204, L.208, E.213, F.220 17 PLIP interactions: 16 interactions with chain E, 1 interactions with chain C, Hydrophobic interactions: E:A.167, E:L.171, E:V.174, E:L.178, E:F.189, E:T.191, E:F.193, E:F.193, E:L.208, E:F.220, E:F.220 Hydrogen bonds: E:T.112, E:Y.113, E:V.114 Salt bridges: E:K.144, C:R.206 Metal complexes: E:H.163

9 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: T.99, S.100 Chain B: Q.23, H.67 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.23, A:S.100, A:S.100 Water bridges: B:A.68 Salt bridges: B:H.67 SO4.5: 4 residues within 4Å: Chain A: K.143, R.218, R.219 Chain B: H.222 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:K.143, A:R.218, B:H.222 SO4.7: 3 residues within 4Å: Chain B: R.93, R.96, H.97 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.96, B:H.97 SO4.8: 4 residues within 4Å: Chain B: Y.16 Chain D: R.197, L.198, E.199 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:L.198, D:E.199, D:E.199, B:Y.16 SO4.11: 4 residues within 4Å: Chain C: R.197, L.198, E.199 Chain E: Y.16 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:L.198, C:E.199, C:E.199, C:E.199 SO4.12: 3 residues within 4Å: Chain A: H.222 Chain C: K.143, R.218 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Salt bridges: A:H.222, C:R.218 SO4.18: 5 residues within 4Å: Chain D: Y.16, R.77 Chain E: R.197, L.198, E.199 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.196, E:L.198, E:E.199, E:E.199, E:E.199 SO4.19: 3 residues within 4Å: Chain D: P.118, E.119, S.120 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:P.118, D:E.119, D:S.120 SO4.25: 4 residues within 4Å: Chain D: K.143, R.218, R.219 Chain E: H.222 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Salt bridges: D:R.218, D:R.219, E:H.222

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: L.31, R.96, H.97 Chain B: D.30 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.96, A:R.96, B:D.30 EDO.9: 4 residues within 4Å: Chain B: K.143, R.218 Chain D: F.220, H.222 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:K.143, D:F.220 EDO.13: 4 residues within 4Å: Chain A: R.197, L.198, E.199 Chain C: Y.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.198, A:E.199 EDO.14: 3 residues within 4Å: Chain C: P.118, E.119, S.120 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.119, C:E.119, C:E.119, C:S.120 EDO.15: 3 residues within 4Å: Chain C: P.111, Q.176 Ligands: HEM.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.176, C:Q.176 EDO.20: 2 residues within 4Å: Chain D: D.27, H.97 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.27, D:D.27 Water bridges: D:H.97 EDO.22: 2 residues within 4Å: Chain E: P.32, G.33 No protein-ligand interaction detected (PLIP) EDO.23: 4 residues within 4Å: Chain C: F.220, H.222 Chain E: K.143, R.218 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:K.143, C:F.220 EDO.24: 3 residues within 4Å: Chain E: P.118, E.119, S.120 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.120, E:S.120

2 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 5 residues within 4Å: Chain A: Q.176, L.178, T.191, F.193 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) IMD.17: 6 residues within 4Å: Chain D: Q.176, K.177, L.178, T.191, F.193 Ligands: HEM.16 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.176

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hofbauer, S. et al., Manipulating conserved heme cavity residues of chlorite dismutase: effect on structure, redox chemistry, and reactivity. Biochemistry (2014)

Release Date

2014-01-15

Peptides

Chlorite dismutase: ABCDE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Chlorite dismutase